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722 lines
31 KiB
722 lines
31 KiB
2 years ago
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:-) GROMACS - gmx mdrun, 2021.3 (-:
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GROMACS is written by:
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Andrey Alekseenko Emile Apol Rossen Apostolov
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Paul Bauer Herman J.C. Berendsen Par Bjelkmar
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Christian Blau Viacheslav Bolnykh Kevin Boyd
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Aldert van Buuren Rudi van Drunen Anton Feenstra
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Gilles Gouaillardet Alan Gray Gerrit Groenhof
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Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
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Aleksei Iupinov Christoph Junghans Joe Jordan
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Dimitrios Karkoulis Peter Kasson Jiri Kraus
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Carsten Kutzner Per Larsson Justin A. Lemkul
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Viveca Lindahl Magnus Lundborg Erik Marklund
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Pascal Merz Pieter Meulenhoff Teemu Murtola
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Szilard Pall Sander Pronk Roland Schulz
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Michael Shirts Alexey Shvetsov Alfons Sijbers
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Peter Tieleman Jon Vincent Teemu Virolainen
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Christian Wennberg Maarten Wolf Artem Zhmurov
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and the project leaders:
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Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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Copyright (c) 2001-2019, The GROMACS development team at
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Uppsala University, Stockholm University and
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the Royal Institute of Technology, Sweden.
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check out http://www.gromacs.org for more information.
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GROMACS is free software; you can redistribute it and/or modify it
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under the terms of the GNU Lesser General Public License
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as published by the Free Software Foundation; either version 2.1
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of the License, or (at your option) any later version.
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GROMACS: gmx mdrun, version 2021.3
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Executable: /usr/local/gromacs/bin/gmx
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Data prefix: /usr/local/gromacs
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Working dir: /home/adit/MySoftware/CMMDE/test/larutan/SistemLarutan
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Process ID: 58606
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Command line:
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gmx -quiet mdrun -deffnm nvep -ntmpi 1 -v true
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GROMACS version: 2021.3
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Verified release checksum is c5bf577cc74de0e05106b7b6426476abb7f6530be7b4a2c64f637d6a6eca8fcb
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Precision: mixed
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Memory model: 64 bit
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MPI library: thread_mpi
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OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
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GPU support: disabled
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SIMD instructions: AVX2_256
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FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
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RDTSCP usage: enabled
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TNG support: enabled
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Hwloc support: disabled
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Tracing support: disabled
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C compiler: /usr/bin/cc GNU 9.3.0
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C compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
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C++ compiler: /usr/bin/c++ GNU 9.3.0
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C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
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Running on 1 node with total 4 cores, 8 logical cores
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Hardware detected:
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CPU info:
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Vendor: Intel
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Brand: 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
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Family: 6 Model: 140 Stepping: 1
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Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
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Number of AVX-512 FMA units: 1 (AVX2 is faster w/o 2 AVX-512 FMA units)
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Hardware topology: Basic
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Sockets, cores, and logical processors:
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Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7]
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
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Lindahl
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GROMACS: High performance molecular simulations through multi-level
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parallelism from laptops to supercomputers
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SoftwareX 1 (2015) pp. 19-25
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
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GROMACS
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In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
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Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
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GROMACS 4.5: a high-throughput and highly parallel open source molecular
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simulation toolkit
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Bioinformatics 29 (2013) pp. 845-54
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
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molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 435-447
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
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Berendsen
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GROMACS: Fast, Flexible and Free
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J. Comp. Chem. 26 (2005) pp. 1701-1719
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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E. Lindahl and B. Hess and D. van der Spoel
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GROMACS 3.0: A package for molecular simulation and trajectory analysis
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J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen
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GROMACS: A message-passing parallel molecular dynamics implementation
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Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
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https://doi.org/10.5281/zenodo.5053201
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-------- -------- --- Thank You --- -------- --------
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The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1
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Input Parameters:
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integrator = md
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tinit = 0
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dt = 0.0005
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nsteps = 10000
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init-step = 0
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simulation-part = 1
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mts = false
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comm-mode = Linear
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nstcomm = 100
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bd-fric = 0
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ld-seed = -1646010373
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emtol = 10
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emstep = 0.01
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niter = 20
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fcstep = 0
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nstcgsteep = 1000
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nbfgscorr = 10
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rtpi = 0.05
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nstxout = 500
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nstvout = 500
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nstfout = 0
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nstlog = 500
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nstcalcenergy = 100
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nstenergy = 500
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nstxout-compressed = 0
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compressed-x-precision = 1000
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cutoff-scheme = Verlet
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nstlist = 10
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pbc = xyz
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periodic-molecules = false
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verlet-buffer-tolerance = 0.005
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rlist = 0.711399
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coulombtype = PME
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coulomb-modifier = Potential-shift
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rcoulomb-switch = 0
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rcoulomb = 0.711399
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epsilon-r = 1
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epsilon-rf = inf
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vdw-type = Cut-off
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vdw-modifier = Potential-shift
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rvdw-switch = 0
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rvdw = 0.711399
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DispCorr = EnerPres
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table-extension = 1
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fourierspacing = 0.16
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fourier-nx = 12
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fourier-ny = 12
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fourier-nz = 12
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pme-order = 4
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ewald-rtol = 1e-05
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ewald-rtol-lj = 0.001
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lj-pme-comb-rule = Geometric
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ewald-geometry = 0
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epsilon-surface = 0
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tcoupl = No
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nsttcouple = -1
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nh-chain-length = 0
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print-nose-hoover-chain-variables = false
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pcoupl = No
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pcoupltype = Isotropic
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nstpcouple = -1
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tau-p = 1
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compressibility (3x3):
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compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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ref-p (3x3):
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ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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refcoord-scaling = No
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posres-com (3):
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posres-com[0]= 0.00000e+00
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posres-com[1]= 0.00000e+00
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posres-com[2]= 0.00000e+00
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posres-comB (3):
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posres-comB[0]= 0.00000e+00
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posres-comB[1]= 0.00000e+00
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posres-comB[2]= 0.00000e+00
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QMMM = false
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qm-opts:
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ngQM = 0
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constraint-algorithm = Lincs
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continuation = true
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Shake-SOR = false
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shake-tol = 0.0001
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lincs-order = 4
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lincs-iter = 1
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lincs-warnangle = 30
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nwall = 0
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wall-type = 9-3
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wall-r-linpot = -1
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wall-atomtype[0] = -1
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wall-atomtype[1] = -1
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wall-density[0] = 0
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wall-density[1] = 0
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wall-ewald-zfac = 3
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pull = false
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awh = false
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rotation = false
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interactiveMD = false
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disre = No
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disre-weighting = Conservative
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disre-mixed = false
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dr-fc = 1000
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dr-tau = 0
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nstdisreout = 100
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orire-fc = 0
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orire-tau = 0
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nstorireout = 100
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free-energy = no
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cos-acceleration = 0
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deform (3x3):
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deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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simulated-tempering = false
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swapcoords = no
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userint1 = 0
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userint2 = 0
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userint3 = 0
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userint4 = 0
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userreal1 = 0
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userreal2 = 0
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userreal3 = 0
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userreal4 = 0
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applied-forces:
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electric-field:
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x:
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E0 = 0
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omega = 0
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t0 = 0
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sigma = 0
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y:
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E0 = 0
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omega = 0
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t0 = 0
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sigma = 0
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z:
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E0 = 0
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omega = 0
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t0 = 0
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sigma = 0
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density-guided-simulation:
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active = false
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group = protein
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similarity-measure = inner-product
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atom-spreading-weight = unity
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force-constant = 1e+09
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gaussian-transform-spreading-width = 0.2
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gaussian-transform-spreading-range-in-multiples-of-width = 4
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reference-density-filename = reference.mrc
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nst = 1
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normalize-densities = true
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adaptive-force-scaling = false
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adaptive-force-scaling-time-constant = 4
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shift-vector =
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transformation-matrix =
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grpopts:
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nrdf: 1209
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ref-t: 0
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tau-t: 0
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annealing: No
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annealing-npoints: 0
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acc: 0 0 0
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nfreeze: N N N
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energygrp-flags[ 0]: 0
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Can not increase nstlist because an NVE ensemble is used
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Using 1 MPI thread
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Using 1 OpenMP thread
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NOTE: Thread affinity was not set.
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System total charge: -0.000
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Will do PME sum in reciprocal space for electrostatic interactions.
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
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A smooth particle mesh Ewald method
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J. Chem. Phys. 103 (1995) pp. 8577-8592
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-------- -------- --- Thank You --- -------- --------
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Using a Gaussian width (1/beta) of 0.227763 nm for Ewald
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Potential shift: LJ r^-12: -5.952e+01 r^-6: -7.715e+00, Ewald -1.406e-05
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Initialized non-bonded Ewald tables, spacing: 7.87e-04 size: 905
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Generated table with 855 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 855 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 855 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Long Range LJ corr.: <C6> 4.1484e-04
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Using SIMD 4x8 nonbonded short-range kernels
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Using a 4x8 pair-list setup:
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updated every 10 steps, buffer 0.000 nm, rlist 0.711 nm
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Using Lorentz-Berthelot Lennard-Jones combination rule
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There are: 404 Atoms
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Center of mass motion removal mode is Linear
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We have the following groups for center of mass motion removal:
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0: rest
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Started mdrun on rank 0 Thu Apr 28 23:06:12 2022
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Step Time
|
||
|
|
0 0.00000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
5.99428e+01 3.56180e+02 1.08426e+02 6.24313e+01 -6.83991e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.66811e+03 -1.26387e+02 -1.88869e+02 -2.39119e+03 1.31181e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.66323e+03 1.12513e+03 -4.53810e+03 2.23858e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
9.98538e+03
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
500 0.25000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
3.25881e+02 2.33194e+02 7.37560e+01 5.42421e+01 -6.90217e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.67396e+03 -2.67822e+01 -1.88869e+02 -2.74424e+03 1.45849e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.80783e+03 1.26905e+03 -4.53878e+03 2.52492e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
-8.07414e+03
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
1000 0.50000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
2.54823e+02 2.79331e+02 6.62055e+01 4.20885e+01 -6.77376e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.64784e+03 1.66437e+01 -1.88869e+02 -2.69774e+03 1.18650e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.76348e+03 1.22477e+03 -4.53871e+03 2.43683e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
1.19652e+03
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
1500 0.75000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
2.34694e+02 2.58759e+02 1.00357e+02 6.36489e+01 -6.95575e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.67504e+03 -8.12779e+01 -1.88869e+02 -2.59040e+03 1.27310e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.75777e+03 1.21899e+03 -4.53878e+03 2.42532e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
7.92818e+02
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
2000 1.00000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
2.96694e+02 3.11317e+02 7.99523e+01 6.08277e+01 -6.78185e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.66116e+03 -5.44866e+01 -1.88869e+02 -2.70159e+03 1.22550e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.74154e+03 1.20322e+03 -4.53832e+03 2.39395e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
-4.60449e+03
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
2500 1.25000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
2.52754e+02 2.93479e+02 8.33528e+01 6.02577e+01 -6.93942e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.67242e+03 -4.20954e+01 -1.88869e+02 -2.68881e+03 1.27354e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.78193e+03 1.24283e+03 -4.53910e+03 2.47276e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
5.62425e+02
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
3000 1.50000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
2.97143e+02 2.69501e+02 8.74233e+01 6.83455e+01 -7.12990e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.69489e+03 7.64003e+01 -1.88869e+02 -2.84679e+03 1.25492e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.81337e+03 1.27466e+03 -4.53871e+03 2.53608e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
9.92100e+02
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
3500 1.75000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
2.89762e+02 2.85771e+02 8.38730e+01 5.10484e+01 -6.79658e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.65433e+03 2.62536e+01 -1.88869e+02 -2.77233e+03 1.29480e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.75614e+03 1.21805e+03 -4.53809e+03 2.42345e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
2.45534e+02
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
4000 2.00000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
2.54975e+02 3.18450e+02 7.77050e+01 5.47855e+01 -6.72105e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.64533e+03 -9.41769e+01 -1.88869e+02 -2.61913e+03 1.42950e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.70537e+03 1.16719e+03 -4.53818e+03 2.32225e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
-3.35894e+03
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
4500 2.25000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
3.33481e+02 3.04330e+02 6.62906e+01 4.86214e+01 -7.00843e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.68251e+03 2.42634e+00 -1.88869e+02 -2.80236e+03 1.24136e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.80146e+03 1.26328e+03 -4.53819e+03 2.51343e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
2.14624e+02
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
5000 2.50000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
3.39930e+02 2.92891e+02 6.96768e+01 4.67481e+01 -6.73381e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.64604e+03 1.34066e+01 -1.88869e+02 -2.77588e+03 1.32168e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.72271e+03 1.18527e+03 -4.53744e+03 2.35823e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
-4.56350e+03
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
5500 2.75000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
2.52495e+02 2.35887e+02 8.33571e+01 5.38983e+01 -6.82821e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.67800e+03 -4.82545e+01 -1.88869e+02 -2.61424e+03 1.47474e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.76308e+03 1.22459e+03 -4.53849e+03 2.43646e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
-1.02638e+03
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
6000 3.00000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
3.13147e+02 2.39011e+02 7.33941e+01 5.34968e+01 -6.90967e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.66805e+03 -2.18502e+01 -1.88869e+02 -2.66729e+03 1.24804e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.74912e+03 1.21058e+03 -4.53853e+03 2.40860e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
1.27520e+02
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
6500 3.25000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
3.09016e+02 2.67246e+02 7.87046e+01 4.63376e+01 -6.84008e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.65858e+03 -2.66303e+01 -1.88869e+02 -2.75379e+03 1.41538e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.79187e+03 1.25337e+03 -4.53850e+03 2.49372e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
-7.49130e+02
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
7000 3.50000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
3.09334e+02 2.45946e+02 7.02546e+01 4.56670e+01 -6.84456e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.65914e+03 2.07605e+01 -1.88869e+02 -2.71921e+03 1.12711e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.76939e+03 1.23114e+03 -4.53825e+03 2.44950e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
1.46120e+03
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
7500 3.75000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
3.49179e+02 2.52384e+02 9.55043e+01 7.34459e+01 -6.93976e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.68927e+03 -1.31437e+01 -1.88869e+02 -2.71160e+03 1.24890e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.71442e+03 1.17642e+03 -4.53800e+03 2.34063e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
-1.39160e+03
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
8000 4.00000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
3.01540e+02 2.89778e+02 7.96111e+01 5.42763e+01 -6.87444e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.67127e+03 2.74904e+01 -1.88869e+02 -2.70070e+03 1.34246e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.68078e+03 1.14344e+03 -4.53733e+03 2.27501e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
1.73129e+03
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
8500 4.25000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
2.89698e+02 2.90379e+02 7.49347e+01 5.73303e+01 -6.88700e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.66852e+03 -7.42266e+01 -1.88869e+02 -2.63272e+03 1.30490e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.72838e+03 1.19016e+03 -4.53823e+03 2.36795e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
6.72412e+02
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
9000 4.50000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
3.07260e+02 2.93818e+02 7.52461e+01 4.52379e+01 -6.95643e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.68113e+03 -1.77533e+01 -1.88869e+02 -2.69938e+03 1.30683e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.74184e+03 1.20329e+03 -4.53855e+03 2.39408e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
-9.66020e+02
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
9500 4.75000
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
3.28822e+02 2.95144e+02 9.61802e+01 6.31835e+01 -6.87580e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.66657e+03 6.08919e+00 -1.88869e+02 -2.85020e+03 1.23600e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.79949e+03 1.26174e+03 -4.53775e+03 2.51039e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
1.07906e+03
|
||
|
|
|
||
|
|
Step Time
|
||
|
|
10000 5.00000
|
||
|
|
|
||
|
|
Writing checkpoint, step 10000 at Thu Apr 28 23:06:14 2022
|
||
|
|
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
3.43095e+02 3.02972e+02 8.56095e+01 5.28222e+01 -6.79941e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.64613e+03 4.37440e+01 -1.88869e+02 -2.85200e+03 1.21920e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.74364e+03 1.20669e+03 -4.53695e+03 2.40084e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
-2.16015e+03
|
||
|
|
|
||
|
|
|
||
|
|
Energy conservation over simulation part #1 of length 5 ns, time 0 to 5 ns
|
||
|
|
Conserved energy drift: 5.67e-04 kJ/mol/ps per atom
|
||
|
|
|
||
|
|
|
||
|
|
<====== ############### ==>
|
||
|
|
<==== A V E R A G E S ====>
|
||
|
|
<== ############### ======>
|
||
|
|
|
||
|
|
Statistics over 10001 steps using 101 frames
|
||
|
|
|
||
|
|
Energies (kJ/mol)
|
||
|
|
Bond Angle Proper Dih. Improper Dih. LJ-14
|
||
|
|
2.92533e+02 2.81408e+02 8.22884e+01 5.44070e+01 -6.86595e+00
|
||
|
|
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
|
||
|
|
-3.66662e+03 -1.00313e+01 -1.88869e+02 -2.72729e+03 1.31145e+02
|
||
|
|
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
|
||
|
|
-5.75789e+03 1.21962e+03 -4.53827e+03 2.42658e+02 -7.58989e+02
|
||
|
|
Pressure (bar)
|
||
|
|
-7.07579e+02
|
||
|
|
|
||
|
|
Total Virial (kJ/mol)
|
||
|
|
4.81421e+02 -5.11129e+00 -4.31531e+00
|
||
|
|
-5.11134e+00 5.01042e+02 2.15936e+01
|
||
|
|
-4.31542e+00 2.15934e+01 5.02170e+02
|
||
|
|
|
||
|
|
Pressure (bar)
|
||
|
|
-6.17553e+02 1.73841e+01 4.89267e+01
|
||
|
|
1.73845e+01 -7.36802e+02 -1.94815e+02
|
||
|
|
4.89275e+01 -1.94814e+02 -7.68383e+02
|
||
|
|
|
||
|
|
|
||
|
|
M E G A - F L O P S A C C O U N T I N G
|
||
|
|
|
||
|
|
NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
|
||
|
|
RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
|
||
|
|
W3=SPC/TIP3p W4=TIP4p (single or pairs)
|
||
|
|
V&F=Potential and force V=Potential only F=Force only
|
||
|
|
|
||
|
|
Computing: M-Number M-Flops % Flops
|
||
|
|
-----------------------------------------------------------------------------
|
||
|
|
Pair Search distance check 86.774298 780.969 1.2
|
||
|
|
NxN Ewald Elec. + LJ [F] 554.883184 36622.290 57.1
|
||
|
|
NxN Ewald Elec. + LJ [V&F] 5.670848 606.781 0.9
|
||
|
|
NxN Ewald Elec. [F] 316.401424 19300.487 30.1
|
||
|
|
NxN Ewald Elec. [V&F] 3.224800 270.883 0.4
|
||
|
|
1,4 nonbonded interactions 1.040104 93.609 0.1
|
||
|
|
Calc Weights 12.121212 436.364 0.7
|
||
|
|
Spread Q Bspline 258.585856 517.172 0.8
|
||
|
|
Gather F Bspline 258.585856 1551.515 2.4
|
||
|
|
3D-FFT 371.717168 2973.737 4.6
|
||
|
|
Solve PME 1.440144 92.169 0.1
|
||
|
|
Shift-X 0.404404 2.426 0.0
|
||
|
|
Bonds 2.910291 171.707 0.3
|
||
|
|
Angles 2.170217 364.596 0.6
|
||
|
|
Propers 1.040104 238.184 0.4
|
||
|
|
Impropers 0.390039 81.128 0.1
|
||
|
|
Virial 0.045349 0.816 0.0
|
||
|
|
Stop-CM 0.040804 0.408 0.0
|
||
|
|
Calc-Ekin 0.808808 21.838 0.0
|
||
|
|
-----------------------------------------------------------------------------
|
||
|
|
Total 64127.080 100.0
|
||
|
|
-----------------------------------------------------------------------------
|
||
|
|
|
||
|
|
|
||
|
|
R E A L C Y C L E A N D T I M E A C C O U N T I N G
|
||
|
|
|
||
|
|
On 1 MPI rank
|
||
|
|
|
||
|
|
Computing: Num Num Call Wall time Giga-Cycles
|
||
|
|
Ranks Threads Count (s) total sum %
|
||
|
|
-----------------------------------------------------------------------------
|
||
|
|
Neighbor search 1 1 1001 0.355 0.996 17.4
|
||
|
|
Force 1 1 10001 1.211 3.396 59.2
|
||
|
|
PME mesh 1 1 10001 0.411 1.151 20.1
|
||
|
|
NB X/F buffer ops. 1 1 19001 0.017 0.049 0.9
|
||
|
|
Write traj. 1 1 21 0.023 0.064 1.1
|
||
|
|
Update 1 1 10001 0.012 0.033 0.6
|
||
|
|
Rest 0.016 0.044 0.8
|
||
|
|
-----------------------------------------------------------------------------
|
||
|
|
Total 2.045 5.733 100.0
|
||
|
|
-----------------------------------------------------------------------------
|
||
|
|
Breakdown of PME mesh computation
|
||
|
|
-----------------------------------------------------------------------------
|
||
|
|
PME spread 1 1 10001 0.176 0.492 8.6
|
||
|
|
PME gather 1 1 10001 0.129 0.363 6.3
|
||
|
|
PME 3D-FFT 1 1 20002 0.051 0.143 2.5
|
||
|
|
PME solve Elec 1 1 10001 0.052 0.145 2.5
|
||
|
|
-----------------------------------------------------------------------------
|
||
|
|
|
||
|
|
NOTE: 17 % of the run time was spent in pair search,
|
||
|
|
you might want to increase nstlist (this has no effect on accuracy)
|
||
|
|
|
||
|
|
Core t (s) Wall t (s) (%)
|
||
|
|
Time: 2.045 2.045 100.0
|
||
|
|
(ns/day) (hour/ns)
|
||
|
|
Performance: 211.244 0.114
|
||
|
|
Finished mdrun on rank 0 Thu Apr 28 23:06:14 2022
|
||
|
|
|